The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Social Network Analysis

Pentatricopeptide repeat proteins: a socket set for organelle gene expression.

Cytoplasmic male sterility (CMS) and nucleus-controlled fertility restoration are widespread plant reproductive features that provide useful tools to exploit heterosis in crops. However, the molecular mechanism underlying this kind of cytoplasmic-nuclear interaction remains unclear. Here, we show in rice (Oryza sativa) with Boro II cytoplasm that an abnormal mitochondrial open reading frame, orf79, is cotranscribed with a duplicated atp6 (B-atp6) gene and encodes a cytotoxic peptide. Expression of orf79 in CMS lines and transgenic rice plants caused gametophytic male sterility. Immunoblot analysis showed that the ORF79 protein accumulates specifically in microspores. Two fertility restorer genes, Rf1a and Rf1b, were identified at the classical locus Rf-1 as members of a multigene cluster that encode pentatricopeptide repeat proteins. RF1A and RF1B are both targeted to mitochondria and can restore male fertility by blocking ORF79 production via endonucleolytic cleavage (RF1A) or degradation (RF1B) of dicistronic B-atp6/orf79 mRNA. In the presence of both restorers, RF1A was epistatic over RF1B in the mRNA processing. We have also shown that RF1A plays an additional role in promoting the editing of atp6 mRNAs, independent of its cleavage function.

Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm Is Caused by a Cytotoxic Peptide and Is Restored by Two Related PPR Motif Genes via Distinct Modes of mRNA Silencing

MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become the subject of intense study. They are a class of post-transcriptional negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in the responses of trees to the stressful environments incurred over their long-term growth. Here, we report the cloning of small RNAs from abiotic stressed tissues of Populus trichocarpa (Ptc) and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, nine families are novel, increasing the number of the known Ptc-miRNA families from 33 to 42. A total of 346 targets was predicted for the cloned Ptc-miRNAs using penalty scores of </=2.5 for mismatched patterns in the miRNA:mRNA duplexes as the criterion. Six of the selected targets were validated experimentally. The expression of a majority of the novel miRNAs was altered in response to cold, heat, salt, dehydration, and mechanical stresses. Microarray analysis of known Ptc-miRNAs identified 19 additional cold stress-responsive Ptc-miRNAs from 14 miRNA gene families. Interestingly, we found that individual miRNAs of a family responded differentially to stress, which suggests that the members of a family may have different functions. These results reveal possible roles for miRNAs in the regulatory networks associated with the long-term growth of tree species and provide useful information for developing trees with a greater level of stress resistance.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2008.03497.x

Stress‐responsive microRNAs in Populus

Nanotechnology has opened new opportunities for delivering bioactive agents. Their physiochemical characteristics, i.e., small size, high surface area, unique composition, biocompatibility and biodegradability, make these nanomaterials an attractive tool for β-carotene delivery. Delivering β-carotene through nanoparticles does not only improve its bioavailability/bioaccumulation in target tissues, but also lessens its sensitivity against environmental factors during processing. Regardless of these benefits, nanocarriers have some limitations, such as variations in sensory quality, modification of the food matrix, increasing costs, as well as limited consumer acceptance and regulatory challenges. This research area has rapidly evolved, with a plethora of innovative nanoengineered materials now being in use, including micelles, nano/microemulsions, liposomes, niosomes, solidlipid nanoparticles, nanostructured lipids and nanostructured carriers. These nanodelivery systems make conventional delivery systems appear archaic and promise better solubilization, protection during processing, improved shelf-life, higher bioavailability as well as controlled and targeted release. This review provides information on the state of knowledge on β-carotene nanodelivery systems adopted for developing functional foods, depicting their classifications, compositions, preparation methods, challenges, release and absorption of β-carotene in the gastrointestinal tract (GIT) and possible risks and future prospects.

Fate of β-Carotene within Loaded Delivery Systems in Food: State of Knowledge.

Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans. GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics.

/pdf/bioactivity-assessment-of-indian-origin-mangrove-4hyb7tz6ws.pdf

Bioactivity Assessment of Indian Origin—Mangrove Actinobacteria against Candida albicans

Extending over decades, research has been of great focus and enormous progress on exploring the ocean for natural products from marine actinobacteria. Attraction towards alternative medicine has led to improvements in natural product discovery. With great potential to survive in extreme environments, marine actinobacteria, efficiently produce an array of metabolites with diverse bioactivity by evolving the secondary metabolic pathways. Exploiting the secondary metabolite producing potential of actinobacteria, many compounds with antitumor, antibacterial, antifungal, antimalarial, antiprotozoal, antiparasitic, antiviral, anti-parasitic, anti-inflammatory activities has been discovered. Efforts in bioprospecting alternative sources of natural products have thus led to several explorations and improvements in technologies which has decreased the bottle neck difficulties in the drug discovery process. Emphasizing on the recent advancements in bioactive compound production in actinobacteria, this paper comprises a review of the available literature, compiles the antitumor compounds from marine actinobacteria with brief discussions and the perspectives to develop better antitumor compounds which would stimulate further research.

/pdf/ocean-dwelling-actinobacteria-as-source-of-antitumor-404bbto3gx.pdf

Ocean Dwelling Actinobacteria as Source of Antitumor Compounds

Nanotechnology, Food Security and Water Treatment

Halotolerant bacterium Bacillus vallismortis (HQ992818) was isolated from saltern sediments in India, and produced significantly high levels extracellular amylase. A detailed investigation on the culture conditions including period of incubation, media pH, and inoculum size in addition to different sources of carbon and nitrogen, metal ions, NaCl, and amino acids was carried out for optimized production. Maximum amylase production (62 U/mL) was attained after 26 h of incubation. The optimized conditions for maximal production of amylase were found to be 1% NaCl, pH 8, temp 37°C, 1% starch, 1% sodium nitrate, phenyl alanine (0.01%) and calcium chloride (10 mM). The biochemical characteristics of the extracellular amylase were studied with respect to change in temperature, pH and metal ions. The enzyme was found to be optimally active in the temperature range of 40–70°C and pH 8. Activation of the enzyme by Ca2+ (135%), Fe2+ (113%) and Mg2+ (109%) occurred at 5 mM concentration and strongly inhibited by Hg2+, Zn2+ and Mn2+ occurred at 10 mM. Significant compatibility of the enzyme with the commercial laundry detergents and the results of washing performance test confirmed its effectiveness. Available data on the optimized culture conditions enables for easily adaptable setup of large scale production of the enzyme for use in detergent formulations.

Kodiveri Muthukaliannan Gothandam

Papers

Fate of β-Carotene within Loaded Delivery Systems in Food: State of Knowledge.

Bioactivity Assessment of Indian Origin—Mangrove Actinobacteria against Candida albicans

Ocean Dwelling Actinobacteria as Source of Antitumor Compounds

Nanotechnology, Food Security and Water Treatment

Insight on biochemical characteristics of thermotolerant amylase isolated from extremophile bacteria Bacillus vallismortis TD6 (HQ992818)